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The ribosomal RNA gene, and particularly its 18S and 25S sequences, have
proven valuable in large-scale phylogenetic analyses. The ITS region of the
ribosomal RNA gene, instead, has not been regarded so useful in this respect.
The main problem has been that these sequences show significant sequence
and length variation and that they have been more or less unalignable beyond
small closely related ...
[++]

The ribosomal RNA gene, and particularly its 18S and 25S sequences, have
proven valuable in large-scale phylogenetic analyses. The ITS region of the
ribosomal RNA gene, instead, has not been regarded so useful in this respect.
The main problem has been that these sequences show significant sequence
and length variation and that they have been more or less unalignable beyond
small closely related groups.
We have determined the common secondary structure of the ITS2 region
and used it to align the sequences over the whole fungal kingdom. Significant
properties of this structure include a central ring structure and three or
four conserved loops – the presence of the ring being the most conserved
feature. The core structure has also revealed the most conserved sites that are
usable in kingdom-wide phylogenetic analyses. Surprisingly, the tree that is
calculated with only the 5.8S ribosomal RNA and the conserved ITS2 sites
has a very high correlation with the Fungal Tree of Life that has been calculated
with four markers and much longer sequences. Furthermore, finding of
the ITS2 secondary structure has revealed a number of group specific sequence
signatures and structural RNA elements that can be used for more
detailed analyses of different subgroups and their phylogeny.
Currently we are (mainly) examining the variation of the loop structures
among the basidiomycetes and linking that to the taxonomy of fungi. Some
examples of current findings will be shown. [--]